RPPanalyzer: Reads, Annotates, and Normalizes Reverse Phase Protein Array Data

Reads in sample description and slide description files and annotates the expression values taken from GenePix results files (text file format used by many microarray scanner and software providers). After normalization data can be visualized as boxplot, heatmap or dotplot.

AuthorHeiko Mannsperger with contributions of Stephan Gade
Date of publication2016-02-11 13:39:56
MaintainerAstrid Wachter <astrid.wachter@med.uni-goettingen.de>
LicenseLGPL
Version1.4.3

View on R-Forge

Man pages

averageData: Average biological replicates over different slides.

calcLinear: Calculates sample concentrations using linear model fit

calcLogistic: Calculates sample concentrations using sigmoid model fit

calcSdc: Calculates the concentration of serial diluted samples

correctBG: Corrects for background in an RPPA data set

correctDilinterc: Dilution series intersect correction

curvePredictSigmoid: Sigmoidal curve prediction.

dataI: Reverse phase protein array rawdata, samples serially diluted

dataII: Reverse phase protein array data, samples from a stimulation...

dataIII: Reverse phase protein array data from original cancer...

dataPreproc: Data preprocessing

getErrorModel: Estimates error model parameters var0 (basal variance) and...

HKdata: Reverse phase protein array data of siRNA transfected cell...

logList: Logarithmize (log2) the first two RPPA list elements, i.e....

normalizeRPPA: Normalizes data in an RPPA data list

pick.high.conc: Select the highest concentration from serialy diluted samples

plotMeasurementsQC: Scatter Plots from an RPPA data

plotQC: Plot target and blank signal from RPPA control samples

plotqq: qq-plot and qq-line of an RPPA data set

plotTimeCourse: Draw time course from RPPA data

plotTimeCourseII: Multiplot function for RPPA time course datasets

read.Data: Read and Annotate RPPA rawdata

remove.arrays: Remove arrays from a RPPA data list

rppa2boxplot: Draws boxplots of groups of an RPPA data set including wilcox...

rppaList2ExpressionSet: Convert RPPA data into Expression Set

rppaList2Heatmap: Draw a heatmap with column side colors from a RPPA data

rppanalyzer-package: Read, annotate and normalize reverse phase protein array data...

S1.gpr: GenePix result files

sampledescription.old: sample description file

sampledescription.txt: sample description file

sample.median: Aggregate the replicates in an RPPA data set

select.measurements: Selects the measurement samples from an RPPA data list

select.sample.group: Selects samples from RPPA data

ser.dil.samples: Reverse phase protein array rawdata, samples serially diluted

simpleBoxplot: Draws boxplots of groups of an RPPA data set.

slidedescription.old: slide description file

slidedescription.txt: slide description file

test.correlation: Tests for correlations in RPPA data

write.Data: writes an RPPA data list into csv file

Functions

analyzeIntercepts Man page
as.my Man page
averageData Man page
calcLinear Man page
calcLogistic Man page
calcSdc Man page
correctBG Man page
correctDilinterc Man page
curvePredictSigmoid Man page
dataI Man page
dataII Man page
dataIII Man page
dataPreproc Man page
getErrorModel Man page
getIntercepts Man page
getSignals Man page
HKdata Man page
logList Man page
normalizeRPPA Man page
pick.high.conc Man page
plotMeasurementsQC Man page
plotQC Man page
plotqq Man page
plotTimeCourse Man page
plotTimeCourseII Man page
read.Data Man page
remove.arrays Man page
rppa2boxplot Man page
rppaList2ExpressionSet Man page
rppaList2Heatmap Man page
RPPanalyzer Man page
RPPanalyzer-package Man page
S1.gpr, S2.gpr, S4.gpr Man page
sampledescription.old Man page
sampledescription.txt Man page
sample.median Man page
select.measurements Man page
select.sample.group Man page
ser.dil.samples Man page
simpleBoxplot Man page
slidedescription.old Man page
slidedescription.txt Man page
test.correlation Man page
write.Data Man page

Files

RPPanalyzer/DESCRIPTION
RPPanalyzer/NAMESPACE
RPPanalyzer/R
RPPanalyzer/R/Sips.R RPPanalyzer/R/annotate.arrays.R RPPanalyzer/R/annotate.samples.R RPPanalyzer/R/array.id.R RPPanalyzer/R/averageData.R RPPanalyzer/R/calcLinear.R RPPanalyzer/R/calcLogistic.R RPPanalyzer/R/calcSdc.R RPPanalyzer/R/correctBG.R RPPanalyzer/R/correctDilinterc.R RPPanalyzer/R/create.ID.col.R RPPanalyzer/R/createColumnIndices.R RPPanalyzer/R/curveFitLinear.R RPPanalyzer/R/curveFitSigmoid.R RPPanalyzer/R/curvePredictLinear.R RPPanalyzer/R/curvePredictSigmoid.R RPPanalyzer/R/dataPreproc.R RPPanalyzer/R/dil.ser.id.R RPPanalyzer/R/g.link.R RPPanalyzer/R/get.Splines.R RPPanalyzer/R/getErrorModel.R RPPanalyzer/R/heatmapcolors.R RPPanalyzer/R/logList.R RPPanalyzer/R/median.raw.R RPPanalyzer/R/norm.BCA.R RPPanalyzer/R/norm.static.I.R RPPanalyzer/R/norm.static.II.R RPPanalyzer/R/norm.texas.R RPPanalyzer/R/normalizeRPPA.R RPPanalyzer/R/pick.high.conc.R RPPanalyzer/R/plotDilutionSeries.R RPPanalyzer/R/plotHeatmap.R RPPanalyzer/R/plotMeasurementsQC.R RPPanalyzer/R/plotQC.R RPPanalyzer/R/plotTimeCourse.R RPPanalyzer/R/plotTimeCourseII.R RPPanalyzer/R/plotqq.R RPPanalyzer/R/protein.con.R RPPanalyzer/R/read.Data.R RPPanalyzer/R/read.gpr.R RPPanalyzer/R/read.sampledescription.R RPPanalyzer/R/read.slidedescription.R RPPanalyzer/R/remove.arrays.R RPPanalyzer/R/rppa2boxplot.R RPPanalyzer/R/rppaList2ExpressionSet.R RPPanalyzer/R/rppaList2Heatmap.R RPPanalyzer/R/sample.median.R RPPanalyzer/R/samples.id.R RPPanalyzer/R/select.measurements.R RPPanalyzer/R/select.sample.group.R RPPanalyzer/R/simpleBoxplot.R RPPanalyzer/R/slides.id.R RPPanalyzer/R/spotbyspot.R RPPanalyzer/R/sub.ID.R RPPanalyzer/R/test.correlation.R RPPanalyzer/R/write.Data.R
RPPanalyzer/build
RPPanalyzer/build/vignette.rds
RPPanalyzer/data
RPPanalyzer/data/HKdata.RData
RPPanalyzer/data/dataI.RData
RPPanalyzer/data/dataII.RData
RPPanalyzer/data/dataIII.RData
RPPanalyzer/data/sampledescription.old.txt.gz
RPPanalyzer/data/ser.dil.samples.RData
RPPanalyzer/data/slidedescription.old.txt.gz
RPPanalyzer/inst
RPPanalyzer/inst/doc
RPPanalyzer/inst/doc/RPPanalyzer.R
RPPanalyzer/inst/doc/RPPanalyzer.pdf
RPPanalyzer/inst/doc/RPPanalyzer.rnw
RPPanalyzer/inst/extdata
RPPanalyzer/inst/extdata/FCF_Slide.gpr
RPPanalyzer/inst/extdata/S1.gpr
RPPanalyzer/inst/extdata/S2.gpr
RPPanalyzer/inst/extdata/S4.gpr
RPPanalyzer/inst/extdata/Slide1.gpr
RPPanalyzer/inst/extdata/Slide2.gpr
RPPanalyzer/inst/extdata/Slide3.gpr
RPPanalyzer/inst/extdata/sampledescription.txt
RPPanalyzer/inst/extdata/slidedescription.txt
RPPanalyzer/man
RPPanalyzer/man/HKdata.Rd RPPanalyzer/man/S1.gpr.Rd RPPanalyzer/man/averageData.Rd RPPanalyzer/man/calcLinear.Rd RPPanalyzer/man/calcLogistic.Rd RPPanalyzer/man/calcSdc.Rd RPPanalyzer/man/correctBG.Rd RPPanalyzer/man/correctDilinterc.Rd RPPanalyzer/man/curvePredictSigmoid.Rd RPPanalyzer/man/dataI.Rd RPPanalyzer/man/dataII.Rd RPPanalyzer/man/dataIII.Rd RPPanalyzer/man/dataPreproc.Rd RPPanalyzer/man/getErrorModel.Rd RPPanalyzer/man/logList.Rd RPPanalyzer/man/normalizeRPPA.Rd RPPanalyzer/man/pick.high.conc.Rd RPPanalyzer/man/plotMeasurementsQC.Rd RPPanalyzer/man/plotQC.Rd RPPanalyzer/man/plotTimeCourse.Rd RPPanalyzer/man/plotTimeCourseII.Rd RPPanalyzer/man/plotqq.Rd RPPanalyzer/man/read.Data.Rd RPPanalyzer/man/remove.arrays.Rd RPPanalyzer/man/rppa2boxplot.Rd RPPanalyzer/man/rppaList2ExpressionSet.Rd RPPanalyzer/man/rppaList2Heatmap.Rd RPPanalyzer/man/rppanalyzer-package.Rd RPPanalyzer/man/sample.median.Rd RPPanalyzer/man/sampledescription.old.Rd RPPanalyzer/man/sampledescription.txt.Rd RPPanalyzer/man/select.measurements.Rd RPPanalyzer/man/select.sample.group.Rd RPPanalyzer/man/ser.dil.samples.Rd RPPanalyzer/man/simpleBoxplot.Rd RPPanalyzer/man/slidedescription.old.Rd RPPanalyzer/man/slidedescription.txt.Rd RPPanalyzer/man/test.correlation.Rd RPPanalyzer/man/write.Data.Rd
RPPanalyzer/vignettes
RPPanalyzer/vignettes/Figure1.png
RPPanalyzer/vignettes/RPPanalyzer.rnw
RPPanalyzer/vignettes/b2-clj4700dn-p2
RPPanalyzer/vignettes/papers_RPPanalyzer.bib
RPPanalyzer/vignettes/workflow_RPPanalyzer.png

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.